tbuckley/cabot-search huggingface dataset:
Cardiac Function Modifies the Impact of Heart Base Dose on Survival: A Voxel-Wise Analysis of Patients With Lung Cancer From the PET-Plan Trial
Authors: Matthew Craddock, Ursula Nestle, Jochem Koenig, Tanja Schimek-Jasch, Stephanie Kremp, Stefan Lenz, Kathryn Banfill, Angela Davey, Gareth Price, Ahmed Salem, Corinne Faivre-Finn, Marcel van Herk, Alan McWilliam
Journal: Journal of Thoracic Oncology (2022)

<h2>Abstract</h2><h3>Introduction</h3> Heart dose has emerged as an independent predictor of overall survival in patients with NSCLC treated with radiotherapy. Several studies have identified the base of the heart as a region of enhanced dose sensitivity and a potential target for cardiac sparing. We present a dosimetric analysis of overall survival in the multicenter, randomized PET-Plan trial (NCT00697333) and for the first time include left ventricular ejection fraction (EF) at baseline as a metric of cardiac function. <h3>Methods</h3> A total of 205 patients with inoperable stage II or III NSCLC treated with 60 to 72 Gy in 2 Gy fractions were included in this study. A voxel-wise image-based data mining methodology was used to identify anatomical regions where higher dose was significantly associated with worse overall survival. Univariable and multivariable Cox proportional hazards models tested the association of survival with dose to the identified region, established prognostic factors, and baseline cardiac function. <h3>Results</h3> A total of 172 patients remained after processing and censoring for follow-up. At 2-years posttreatment, a highly significant region was identified within the base of the heart (<i>p</i> < 0.005), centered on the origin of the left coronary artery and the region of the atrioventricular node. In multivariable analysis, the number of positron emission tomography–positive nodes (<i>p</i> = 0.02, hazard ratio = 1.13, 95% confidence interval: 1.02–1.25) and mean dose to the cardiac subregion (<i>p</i> = 0.02, hazard ratio = 1.11 Gy<sup>−1</sup>, 95% confidence interval: 1.02–1.21) were significantly associated with overall survival. There was a significant interaction between EF and region dose (<i>p</i> = 0.04) for survival, with contrast plots revealing a larger effect of region dose on survival in patients with lower EF values. <h3>Conclusions</h3> This work validates previous image-based data mining studies by revealing a strong association between dose to the base of the heart and overall survival. For the first time, an interaction between baseline cardiac health and heart base dose was identified, potentially suggesting preexisting cardiac dysfunction exacerbates the impact of heart dose on survival.
Abstract A012: Targeting the dysregulation of transcription and splicing in Ewing sarcoma
Authors: Liesl A. Lawrence, Henry Miller, Alexander Bishop
Journal: Clinical Cancer Research (2022)

Abstract The goals of this study are to investigate how EWS-FLI1 disrupts regulation of transcription and splicing in Ewing sarcoma, and to evaluate this dysregulation as a potential therapeutic target. Ewing Sarcoma is an aggressive pediatric bone and soft tissue cancer driven primarily by the EWS-FLI1 fusion oncogene. EWS-FLI1 acts as an oncogenic transcription factor and also interferes with normal regulation of transcription and transcription-associated RNA processing. Chemotherapy has substantially improved overall survival, but the prognosis is still very poor for those with metastatic or recurrent disease, and toxicity is a major concern in pediatric patients. Consequently, effective, less toxic, targeted treatment strategies are much needed. We performed a genome-wide RNAi screen in the Ewing sarcoma cell line TC32 and found that one of the top pathways required for cell survival was RNA processing/splicing. Previous studies have reported increased amounts of alternative splicing events in Ewing sarcoma. RNA processing, including splicing, is functionally coupled with transcription. We recently reported that Ewing sarcoma cells have high levels of phosphorylated RNA polymerase II and increased transcription activity, accumulate R-loops, and fail to regulate transcription appropriately in response to DNA damage. We proposed that EWS-FLI1 driven hyper-activation of transcription causes a targetable dependence on RNA splicing in Ewing sarcoma. Ewing sarcoma cells showed increased sensitivity to depletion of key splicing factors compared to mesenchymal stem cell controls; this was partially rescued by depleting EWS-FLI1 or by overexpressing RNASEH1, which degrades R-loops. Ewing sarcoma cells were extremely sensitive to splicing inhibition, which showed synergy with multiple chemotherapeutic agents. Splicing inhibition in Ewing sarcoma cells caused cell cycle arrest, induced apoptosis, and altered global gene expression, alternative splicing, and R-loop profiles as seen by RNA-seq and DRIP-seq. This work provides novel insight into transcription regulation and its dysregulation by EWS-FLI1. In addition, our results point to RNA splicing as a potential new therapeutic target in Ewing sarcoma, which has the potential to benefit all Ewing sarcoma patients, especially those with chemo-resistant disease. Citation Format: Liesl A. Lawrence, Henry Miller, Alexander Bishop. Targeting the dysregulation of transcription and splicing in Ewing sarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A012.
Abstract A026: PROX1 transcription factor regulates rhabdomyosarcoma growth, myogenic properties and therapeutic targets
Authors: Nebeyu Y. Gizaw, Pauliina Kallio, Erika Gucciardo, Caj Haglund, Tom Bohling, Kaisa Lehti, Mika Sampo, Kari Alitalo, Riikka Kivela
Journal: Clinical Cancer Research (2022)

Abstract Rhabdomyosarcoma (RMS) is an aggressive pediatric soft tissue cancer with features of skeletal muscle. Because of poor survival of RMS patients and severe long-term side effects of RMS therapies, novel RMS therapies are urgently needed. Here we show that the PROX1 transcription factor is highly expressed in RMS tumors regardless of their cell type of origin. We demonstrate that PROX1 is needed for RMS cell clonogenicity, growth and tumor formation. PROX1 gene silencing repressed several myogenic and tumorigenic transcripts and altered the RD (ERMS) transcriptome to resemble that of benign mesenchymal stem cells. Importantly, we found that fibroblast growth factor receptors (FGFR) mediated the growth effects of PROX1 in RMS. Because of receptor cross-compensation, inhibition of either alone did not mimic the effects of PROX1 silencing, whereas a pan-FGFR inhibitor ablated RMS cell proliferation and decreased tumor xenograft growth. Our findings uncover the critical role of PROX1 in RMS and offer new insights to the mechanisms that regulate RMS development and growth. As FGFR inhibitors have already been tested in unrelated clinical trials, our findings provide a new promising option for RMS treatment. Citation Format: Nebeyu Y. Gizaw, Pauliina Kallio, Erika Gucciardo, Caj Haglund, Tom Bohling, Kaisa Lehti, Mika Sampo, Kari Alitalo, Riikka Kivela. PROX1 transcription factor regulates rhabdomyosarcoma growth, myogenic properties and therapeutic targets [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A026.
Abstract IA008: Altering the T cell receptor repertoire in the sarcoma tumor immune microenvironment
Authors: Seth M. Pollack, Y. Dave Seo
Journal: Clinical Cancer Research (2022)

Abstract Our lab has been interested in characterizing the T cell receptor (TCR) repertoire of sarcoma subtypes as well as characterizing their immune infiltrates and studying the changes that occur on experimental immunotherapies. In this trial, 15 patients with metastatic soft tissue sarcoma STS patients with a superficial injectable lesion were treated weekly with an intratumoral (IT) toll like receptor 4 (TLR4) agonist Glucopyranosyl Lipid Adjuvant (GLA) for 8-12 weeks plus concurrent radiotherapy. Core biopsies and blood were collected pre and post treatment, and immune analysis was performed by T cell receptor (TCR) sequencing and multiplex IHC. RECIST v1.1 and CTCAE guidelines were used to monitor clinical outcomes. No grade 3 or higher treatment-related toxicity was observed, and local tumor control was achieved in 93% (14/15). 6 (40%) had overall stable disease after IT GLA, and one had complete regression of injected tumor. 3 other patients had long term control of injected tumor past 250 days, during which the uninjected STS had progression despite radiation. In patients with durable local control after IT GLA, multiplex IHC demonstrated increased CD4 and CD8 T cell infiltration, as well as decrease in regulatory T cells. In patient #5-6, TCR sequencing revealed 5-fold increase in PBMC clonality, with selective clonal expansion of T cells present in pre-treatment biopsy. In patient #10-6 (local control to 370 days), there was clonal expansion of T cells within TME which were also found in post treatment PBMC; matched single cell sequencing revealed these clones to be CD4 T cells with Th1 gene signatures. In this trial we found that GLA with radiation induced effective local control of superficial, metastatic STS lesion, inducing a shift in the TME towards an inflammatory state with strong infiltration of T cells. There was selective expansion of clones present in pre-treatment TME in circulating PBMC post IT GLA, isolated to be Th1 cells in one patient. This suggests induction of adaptive anti-tumor response, which may further be enhanced by combination with other immunomodulators. Citation Format: Seth M. Pollack, Y. Dave Seo. Altering the T cell receptor repertoire in the sarcoma tumor immune microenvironment [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA008.
Abstract IA026: Epigenetic and genomic features define distinct cellular states with possible therapeutic relevance in osteosarcoma
Authors: E. Alejandro Sweet-Cordero
Journal: Clinical Cancer Research (2022)

Abstract The Osteosarcoma (OS) genome is characterized by aneuploidy and dramatic structural rearrangements often leading to copy number gain and loss. Currently, all patients with osteoblastic OS at diagnosis are treated with the same highly toxic chemotherapy and no clinically relevant subtypes have been identified. While there is significant heterogeneity at the genome level between patients, less is known regarding epigenetic heterogeneity and how this may impact critical phenotypes such as therapy response and metastasis. To characterize the osteosarcoma epigenome, we integrated ATAC-seq and RNA-seq across a unique set of patient samples, PDXs and PDX-derived cell lines obtained across the disease continuum and including biopsies, resections, and metastasis. ATACseq analysis revealed the presence of two distinct epigenetic cell states (C1 and C2). Associating the differential genomic regions to likely regulated genes, the enriched pathways of Cluster 1 (C1) are related to mesenchymal cell proliferation, skeletal system morphogenesis, osteoblast differentiation, and Wnt signaling pathway. In contrast, Cluster 2 (C2) enriched pathways are related to cell motility and migration, extracellular matrix organization and regulation of protein serine/threonine kinase activity. Furthermore, accessible chromatin regions were enriched for a distinct set of transcription factor binding sites. We then assessed whether these epigenetic states were associated with response to targeted therapies. We identified unique vulnerability of C1 cell lines to AURK inhibitors whereas C2 cell lines had evidence for upregulation of MAPK and were vulnerable to treatment with trametinib. ATACseq analysis of PDX and a limited number of patient samples confirmed that these subtypes of OS also likely exist in patient tumors. In parallel to these studies, we have also carried out extensive additional analysis of vulnerability of OS cell ines to a wide range of targeted therapies. We find evidence for significant response to several inhibitors of the ATR-WEE1-CHK1 pathway nominating this as a potential novel vulnerability for OS. Therapeutic relevance of these findings is currently being explores in an orthotopic metastasis model of OS. Overall, our findings may define new subtypes of osteosarcoma with unique therapeutic vulnerabilities. Citation Format: E. Alejandro Sweet-Cordero. Epigenetic and genomic features define distinct cellular states with possible therapeutic relevance in osteosarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA026.
Abstract PR008: The 3D epigenome of rhabdomyosarcoma
Authors: Berkley E. Gryder, Issra Osman, Adam Durbin, Jun Qi
Journal: Clinical Cancer Research (2022)

Abstract Rhabdomyosarcoma (RMS) is driven by transcription factors that set up super-enhancers: large clusters of transcriptional machinery accumulated at oncogenes. Super-enhancers are also the key vulnerability of RMS, as we have revealed by CRISPR screening and chemical genomics. However, the identification of super-enhancers is inconsistent, because they are extracted from 1-dimensional ChIP-seq data, but are in fact 3D genomic objects (“super-clusters”) that form biomolecular condensates (phase-separated droplets). We have now applied new 3D genomics approaches to enable proper discovery of these epigenomic features, also yielding proper enhancer-gene connectivity maps. Furthermore, super-clusters are co-built by transcription factors recruiting p300 (acetylation writer) and BRD4 (acetylation reader). We have generated preliminary evidence that directly perturbing/degrading p300 and BRD4 are the most effective and selective means to shut down super-clusters at all oncogenes driving this childhood cancer. We applied Absolute Quantification of Architecture (AQuA) HiChIP, and were able to uncover the drug-induced 3D folding abnormalities that selectively halt RNA-Polymerase 2 at super-cluster driven oncogenes in this sarcoma. Citation Format: Berkley E. Gryder, Issra Osman, Adam Durbin, Jun Qi. The 3D epigenome of rhabdomyosarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr PR008.
Abstract B018: A robust system to study human soft-tissue sarcoma lung metastasis
Authors: Maria Muñoz, Janai R. Carr-Ascher
Journal: Clinical Cancer Research (2022)

Abstract Soft-tissue sarcoma (STS) is a rare connective tissue cancer that encompasses over 50 distinct subtypes including liposarcoma, undifferentiated pleomorphic sarcoma (UPS) and pleomorphic rhabdomyosarcoma. While these subtypes are histologically and genetically different, all are capable of metastasizing into the lungs. However, the mechanisms of metastasis are poorly understood, and patients with metastatic disease have low survival rates. Current statistics show that these patients have a 15% 5-year relative survival rate. It is crucial to understand the mechanisms of metastasis to improve patient therapeutics and survival. Thus, we developed a robust system to enrich and study spontaneous metastatic cells in STS. To do this, we started by screening multiple cell lines for metastatic activity in-vivo. First, immunocompromised mice were injected in the thigh (intramuscularly) with tumor cells. The liposarcoma cell line SW872 gave rise to metastatic tumors in the lung although with limited penetrance and a long latency. Therefore, we identified a mouse with a high metastatic burden and generated a cell line from the primary tumor that was highly metastatic. These serially passaged cells were injected intramuscularly into the thigh of immunocompromised mice and allowed to spontaneously metastasize. This resulted in earlier detection of tumors, and a decreased latency to metastatic disease. For downstream analysis, we enriched the metastatic population resulting from the serially passaged tumor. This was accomplished by first digesting lungs, then depleting mouse cells with magnetic beads. We further enriched the population by sorting HLA-APC positive (human) cells using fluorescence-activated cell sorting (FACS). This process was necessary to reduce mouse cell contamination, and ensure we solely analyzed human cells. Afterwards, metastatic cells can be compared to the primary tumor using RNA, ATAC or Whole-Exome sequencing. We hypothesize that a comparison between the primary and metastatic tumors will identify pathways that allow cells to metastasize. These pathways can be targeted in future therapeutics to improve patient outcomes. This system can also be applied to other STS subtypes. Overall, our robust system allows us to study spontaneous lung metastases, is reflective of the human disease and will provide insight into the mechanisms of metastasis in STS. Citation Format: Maria Muñoz, Janai R. Carr-Ascher. A robust system to study human soft-tissue sarcoma lung metastasis [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr B018.
Most Arginase-1 Positive Cells Are Likely Injured S3 Proximal Tubular Cells Carrying Upregulated Phagocytotic Capacity rather than M2 Macrophages—Too Many To Be True
Authors: Ping L. Zhang, Neal B. Blatt, Hassan D. Kanaan, Larysa T. Wickman
Journal: Journal of the American Society of Nephrology (2022)

Shin et al.1 recently published a very interesting study demonstrating mice with selective knockout arginase-1 (Arg1mko) in myelomonocytic cells had decreased tubular repair and decreased survival after ischemia-reperfusion injury (IRI). Control mice (Arg1con) showed extensive arginase-1 expression in the medulla but Arg1mko mice did not (figures 1E, left panels, and 4A in Shin et al.1). The researchers concluded that arginase-1–rich macrophages (M2) were required for the S3 tubular cell repair after IRI. However, when we looked at the histology of renal sections from both Arg1con and Arg1mko in figure 2D (right enlarged panels), the main cells forming tubular configurations were S3 proximal tubular epithelial cells in both types of mice, similar to what we have demonstrated in the rat model of IRI.2 It is not possible for there to be so many arginase-1–positive macrophages (M2) in figure 2D (right enlarged panels) to correspond to the starry-sky amount of arginase-1 expression shown in both figure 1E (Arg1con, left panel) and figure 4A. In addition, their F4/80 (an M1 macrophage marker) staining was also extensively positive in both Arg1con and Arg1mko of figure 1E (left panels). There appear to be too many F4/80-staining cells for these cells to be true macrophages after IRI on the basis of the histology images of figure 2D (right enlarged panels). We think that most arginase-1–positive cells after IRI were likely from injured S3 proximal tubules. We suggest the authors can easily confirm our speculation by double restaining the kidney sections using arginase-1 and PAX-8 (a nuclear marker for renal tubules). We hypothesize the extensive positive F4/80 staining in figure 1E was most likely positive in the injured S3 proximal tubules of both types of mice. Injured proximal tubules are well known to have a phagocytic capacity, with upregulated kidney injury molecule-1 acting as receptors that prevent activation of inflammation.3,4 Higher expression of kidney injury molecule-1 in the injured proximal tubules is associated with better recovered renal function.5,6 In addition, the injured proximal tubules are positive for lysosome marker CD68, confirming the phagocytic capability of injured proximal tubules (our unpublished data). In summary, Shin et al.1 have provided critical evidence of arginase-1 in renal tubular repair, but we suggest they clarify whether the multiple arginase-1–rich cells seen after IRI are injured S3 proximal tubular cells or M2 macrophages. Further studies may pave the way for understanding how arginase-1 interacts with some repairing molecules, including GM-CSF, in injured proximal tubules. Disclosures N.B. Blatt reports having ownership interest in Lycera (ownership interest ended November 2021). All remaining authors have nothing to disclose. Funding None.
Steroid-Resistant Nephrotic Syndrome–Associated MYO1E Mutations Have Differential Effects on Myosin 1e Localization, Dynamics, and Activity
Authors: Pei-Ju Liu, Laura K. Gunther, Michael E. Garone, Chunling Zhang, Diana Perez, Jing Bi-Karchin, Christopher D. Pellenz, Sharon E. Chase, Maria F. Presti, Eric L. Plante, Claire E. Martin, Svjetlana Lovric, Christopher M. Yengo, Friedhelm Hildebrandt, Mira Krendel
Journal: Journal of the American Society of Nephrology (2022)

Myo1e is a nonmuscle motor protein enriched in podocytes. Mutations in MYO1E are associated with steroid-resistant nephrotic syndrome (SRNS). Most of the MYO1E variants identified by genomic sequencing have not been functionally characterized. Here, we set out to analyze two mutations in the Myo1e motor domain, T119I and D388H, which were selected on the basis of protein sequence conservation.EGFP-tagged human Myo1e constructs were delivered into the Myo1e-KO mouse podocyte-derived cells via adenoviral infection to analyze Myo1e protein stability, Myo1e localization, and clathrin-dependent endocytosis, which is known to involve Myo1e activity. Furthermore, truncated Myo1e constructs were expressed using the baculovirus expression system and used to measure Myo1e ATPase and motor activity in vitro.Both mutants were expressed as full-length proteins in the Myo1e-KO cells. However, unlike wild-type (WT) Myo1e, the T119I variant was not enriched at the cell junctions or clathrin-coated vesicles (CCVs). In contrast, D388H variant localization was similar to that of WT. The rate of dissociation of the D388H variant from cell-cell junctions and CCVs was decreased, suggesting this mutation affects Myo1e interactions with binding partners. ATPase activity and ability to translocate actin filaments were drastically reduced for the D388H mutant, supporting findings from cell-based experiments.T119I and D388H mutations are deleterious to Myo1e functions. The experimental approaches used in this study can be applied to future characterization of novel MYO1E variants associated with SRNS.
Expression of Concern: Central Role for Adipocyte Na,K-ATPase Oxidant Amplification Loop in the Pathogenesis of Experimental Uremic Cardiomyopathy
Journal: Journal of the American Society of Nephrology (2022)

Komal Sodhi, Xiaoliang Wang, Muhammad Aslam Chaudhry, Hari Vishal Lakhani, Mishghan Zehra, Rebecca Pratt, Athar Nawab, Cameron L. Cottrill, Brian Snoad, Fang Bai, James Denvir, Jiang Liu, Juan R. Sanabria, Zijian Xie, Nader G. Abraham and Joseph I. Shapiro. Central Role for Adipocyte Na,K-ATPase
Exercise as airway clearance therapy (ExACT) in cystic fibrosis: a UK-based e-Delphi survey of patients, caregivers and health professionals
Authors: Zoe Louise Saynor, Steve Cunningham, Lisa Morrison, Eleanor Main, Ioannis Vogiatzis, Simon Reid, Donald Urquhart
Journal: Thorax (2022)

Replacing traditional airway clearance therapy (tACT) with exercise (ExACT) in people with cystic fibrosis (pwCF) is a top research priority. A UK-based e-Delphi consensus was performed to inform the type(s), duration and intensity of ExACT. The expert panel comprised CF physiotherapists, doctors, pwCF and parents/partners. Exercise ACT was considered to be aerobic activity, of at least 20 min duration and intense enough to elicit deep breathing. Consensus was reached that assessment breaths, coughs and huffs should accompany exercise to remove loose secretions, with support for trials to investigate ExACT versus tACT during times of stable disease but not pulmonary exacerbations.